Volume and hydration changes of DNA-ligand interactions

Biophysical Chemistry

Volumn 125, Issue 2-3, 2007, Pages 471-482

  Shi, Xuesong ^a   Macgregor Jr , Robert B ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Binding parameters; DNA ligand interactions; Hydration; Hydrostatic pressure; Volumetric parameters

Indexed keywords

4 [5 (4 METHYL 1 PIPERAZINYL)[2,5' BI 1H BENZIMIDAZOL] 2' YL]PHENOL; DAUNORUBICIN; DNA; ETHIDIUM BROMIDE; LIGAND; POLYMER; PROPIDIUM IODIDE;

ARTICLE; BINDING AFFINITY; DNA SEQUENCE; DRUG DESIGN; EQUILIBRIUM CONSTANT; FLUORESCENCE; HYDRATION; HYDROSTATIC PRESSURE; LIGAND BINDING; MOLECULAR INTERACTION; PRIORITY JOURNAL; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

BINDING SITES; DNA; INTERCALATING AGENTS; LIGANDS; NUCLEIC ACID CONFORMATION; THERMODYNAMICS; WATER;

EID: 33846303216     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.10.011     Document Type: Article

References (62)

1. Spolar R.S., Ha J.H., and Record M.T. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 8382-8385
2. Ha J.H., Spolar R.S., and Record M.T. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. J. Mol. Biol. 209 (1989) 801-816
3. Ren J.S., Jenkins T.C., and Chaires J.B. Energetics of DNA intercalation reactions. Biochemistry 39 (2000) 8439-8447
4. Spolar R.S., and Record M.T. Coupling of local folding to site-specific binding of proteins to DNA. Science 263 (1994) 777-784
5. Haq I., Jenkins T.C., Chowdhry B.Z., Ren J.S., and Chaires J.B. Parsing free energies of drug-DNA interactions. Methods Enzymol. 323 (2000) 373-405
6. Haq I. Part II: the thermodynamics of drug-biopolymer interaction- thermodynamics of drug-DNA interactions. Arch. Biochem. Biophys. 403 (2002) 1-15
7. Chaires J.B. Energetics of drug-DNA interactions. Biopolymers 44 (1998) 201-215
8. Berman H.M. Hydration of DNA- take 2. Curr. Opin. Struct. Biol. 4 (1994) 345-350
9. Marky L.A., and Macgregor R.B. Hydration of dA.dT polymers- role of water in the thermodynamics of ethidium and propidium intercalation. Biochemistry 29 (1990) 4805-4811
10. Tang G.Q., Tanaka N., and Kunugi S. Effects of pressure on the DNA minor groove binding of Hoechst 33258. Bull. Chem. Soc. Jpn. 71 (1998) 1725-1730
11. Tang G.Q., Tanaka N., and Kunugi S. Salt effects on fluorescence spectral shifts of DNA-bound Hoechst 33258 and reaction volumes of the minor groove binding. Bull. Chem. Soc. Jpn. 72 (1999) 1129-1137
12. Han F.X., and Chalikian T.V. Hydration changes accompanying nucleic acid intercalation reactions: volumetric characterizations. J. Am. Chem. Soc. 125 (2003) 7219-7229
13. Rentzeperis D., Kupke D.W., and Marky L.A. Differential hydration of homopurine sequences relative to alternating purine pyrimidine sequences. Biopolymers 32 (1992) 1065-1075
14. Marky L.A., and Kupke D.W. Probing the hydration of the minor groove of A•T synthetic DNA polymers by volume and heat changes. Biochemistry 28 (1989) 9982-9988
15. Chalikian T.V., Plum G.E., Sarvazyan A.P., and Breslauer K.J. Influence of drug-binding on DNA hydration- acoustic and densimetric characterizations of netropsin binding to the poly(dAdT)•poly(dAdT) and poly(dA)•poly(dT) duplexes and the poly(dT)•poly(dT)•poly(dT) triplex at 25-Degrees-C. Biochemistry 33 (1994) 8629-8640
16. Bresloff J.L., and Crothers D.M. Equilibrium studies of ethidium-polynucleotide interactions. Biochemistry 20 (1981) 3547-3553
17. Schmechel D., and Crothers D.M. Kinetic and hydrodynamic studies of complex of proflavine with poly A•poly U. Biopolymers 10 (1971) 465-480
18. Pohl F.M., and Jovin T.M. Salt-induced cooperative conformational change of a synthetic DNA- equilibrium and kinetic studies with poly(dGdC). J. Mol. Biol. 67 (1972) 375-396
19. Bresloff J.L., and Crothers D.M. DNA-ethidium reaction-kinetics- demonstration of direct ligand transfer between DNA binding-sites. J. Mol. Biol. 95 (1975) 103-123
20. Patel D.J., and Canuel L.L. Netropsin-poly(dAdT) complex in solution- structure and dynamics of antibiotic-free base pair regions and those centered on bound netropsin. Proc. Natl. Acad. Sci. U. S. A. 74 (1977) 5207-5211
21. Suh D., Oh Y.K., Hur M.W., Ahn B., and Chaires J.B. Daunomycin binding to deoxypolynucleotides with alternating sequences: complete thermodynamic profiles of heterogeneous binding sites. Nucleosides Nucleotides Nucleic Acids 21 (2002) 637-649
22. Loontiens F.G., Regenfuss P., Zechel A., Dumortier L., and Clegg R.M. Binding characteristics of Hoechst-33258 with calf thymus DNA, poly[d(A-T)], and d(CCGGAATTCCGG): multiple stoichiometries and determination of tight-binding with a wide spectrum of site affinities. Biochemistry 29 (1990) 9029-9039
23. McGhee J.D., and von Hippel P.H. Theoretical aspects of DNA-protein interactions- cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86 (1974) 469-489
24. Correia J.J., and Chaires J.B. Analysis of drug-DNA binding isotherms: a Monte Carlo approach. MethodS Enzymol. 240 (1994) 593-614
25. Shi X.S., and Macgregor Jr. R.B. Temperature dependence of the volumetric parameters of drug binding to poly[d(A-T)]•poly[d(A-T)] and poly(dA)•poly(dT). Biophys. J. 90 (2006) 1729-1738
26. Wilson W.D., Wang Y.H., Krishnamoorthy C.R., and Smith J.C. Poly(dT) •Poly(dT) exists in an unusual conformation under physiological conditions- propidium binding to poly(dA)•poly(dT) and poly[d(A-T)]•poly[d(A-T)]. Biochemistry 24 (1985) 3991-3999
27. Macgregor R.B., Clegg R.M., and Jovin T.M. Pressure-jump study of the kinetics of ethidium-bromide binding to DNA. Biochemistry 24 (1985) 5503-5510
28. Xodo L.E., Manzini G., Ruggiero J., and Quadrifoglio F. On the interaction of daunomycin with synthetic alternating DNAs- sequence specificity and poly-electrolyte effects on the intercalation equilibrium. Biopolymers 27 (1988) 1839-1857
29. Herrera J.E., and Chaires J.B. A premelting conformational transition in poly(dA) •poly(dT) coupled to daunomycin binding. Biochemistry 28 (1989) 1993-2000
30. Chaires J.B. Biophysical chemistry of the daunomycin-DNA interaction. Biophys. Chem. 35 (1990) 191-202
31. Chaires J.B. Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides. Biochemistry 22 (1983) 4204-4211
32. Breslauer K.J., Remeta D.P., Chou W.Y., Ferrante R., Curry J., Zaunczkowski D., Snyder J.G., and Marky L.A. Enthalpy entropy compensations in drug DNA-binding studies. Proc. Natl. Acad. Sci. U. S. A. 84 (1987) 8922-8926
33. Harris S.A., Gavathiotis E., Searle M.S., Orozco M., and Laughton C.A. Cooperativity in drug-DNA recognition: a molecular dynamics study. J. Am. Chem. Soc. 123 (2001) 12658-12663
34. Rao K.E., and Lown J.W. Molecular recognition between ligands and nucleic-acids- DNA-binding characteristics of analogs of Hoechst 33258 designed to exhibit altered base and sequence recognition. Chem. Res. Toxicol. 4 (1991) 661-669
35. Manning G.S. Molecular theory of polyelectrolyte solutions with applications to electrostatic properties of polynucleotides. Q. Rev. Biophys. 11 (1978) 179-246
36. Record M.T., Anderson C.F., and Lohman T.M. Thermodynamic analysis of ion effects on binding and conformational equilibria of proteins and nucleic-acids- roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11 (1978) 103-178
37. Record M.T., Lohman T.M., and DeHaseth P. Ion effects on ligand-nucleic acid interactions. J. Mol. Biol. 107 (1976) 145-158
38. Chou W.Y., Marky L.A., Zaunczkowski D., and Breslauer K.J. The thermodynamics of drug-DNA interactions- ethidium-bromide and propidium iodide. J. Biomol. Struct. Dyn. 5 (1987) 345-359
39. Chaires J.B. Dissecting the free energy of drug binding to DNA. Anti-Cancer Drug Des. 11 (1996) 569-580
40. Luque I., and Freire E. Structure-based prediction of binding affinities and molecular design of peptide ligands. Methods Enzymol. 295 (1998) 100-127
41. Baldwin R.L. Temperature-dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. U. S. A. 83 (1986) 8069-8072
42. Pierotti R.A. Scaled particle theory of aqueous and non-aqueous solutions. Chem. Rev. 76 (1976) 717-726
43. Kharakoz D.P. Partial molar volumes of molecules of arbitrary shape and the effect of hydrogen-bonding with water. J. Solution Chem. 21 (1992) 569-595
44. Chalikian T.V. Structural thermodynamics of hydration. J. Phys. Chem. B 105 (2001) 12566-12578
45. Chalikian T.V. Hydrophobic polar groups tendencies of as a major force in molecular recognition. Biopolymers 70 (2003) 492-496
46. Drew H.R., and Dickerson R.E. Structure of a B-DNA dodecamer 3. Geometry of hydration. J. Mol. Biol. 151 (1981) 535-556
47. Nelson H.C.M., Finch J.T., Luisi B.F., and Klug A. The structure of an oligo(dA).Oligo(dT) tract and its biological implications. Nature 330 (1987) 221-226
48. SantaLucia J., Allawi H.T., and Seneviratne A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35 (1996) 3555-3562
49. SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 1460-1465
50. Frank-Kamenetskii M.D. Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution. Biopolymers 10 (1971) 2623-2624
51. Dubins D.N., and Macgregor R.B. Volumetric properties of the formation of double stranded DNA: a nearest-neighbor analysis. Biopolymers 73 (2004) 242-257
52. Wang A.H.J., Ughetto G., Quigley G.J., and Rich A. Interactions between an anthracycline antibiotic and DNA- molecular-structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-Å resolution. Biochemistry 26 (1987) 1152-1163
53. Frederick C.A., Williams L.D., Ughetto G., Vandermarel G.A., Vanboom J.H., Rich A., and Wang A.H.J. Structural comparison of anticancer drug DNA complexes- adriamycin and daunomycin. Biochemistry 29 (1990) 2538-2549
54. Nunn C.M., Vanmeervelt L., Zhang S., Moore M.H., and Kennard O. DNA drug-interactions- the crystal-structures of d(TGTACA) and d(TGATCA) complexed with daunomycin. J. Mol. Biol. 222 (1991) 167-177
55. Moore M.H., Hunter W.N., Destaintot B.L., and Kennard O. DNA-drug interactions- the crystal-structure of d(CGATCG) complexed with daunomycin. J. Mol. Biol. 206 (1989) 693-705
56. Chalikian T.V., Volker J., Srinivasan A.R., Olson W.K., and Breslauer K.J. The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques. Biopolymers 50 (1999) 459-471
57. Jain S.C., Tsai C., and Sobell H.M. Visualization of drug-nucleic acid interactions at atomic resolution. 2. Structure of an ethidium-dinucleoside monophosphate crystalline complex, ethidium- 5-iodocytidylyl (3′-5′) guanosine. J. Mol. Biol. 114 (1977) 317-331
58. Macgregor R.B., Clegg R.M., and Jovin T.M. Viscosity dependence of ethidium-DNA intercalation kinetics. Biochemistry 26 (1987) 4008-4016
59. 2 duplex: calorimetric and spectroscopic studies. J. Mol. Biol. 271 (1997) 244-257
60. 2: volumetric, calorimetric, and spectroscopic characterizations. Biochemistry 44 (2005) 9785-9794
61. Kiser J.R., Monk R.W., Smalls R.L., and Petty J.T. Hydration changes in the association of Hoechst 33258 with DNA. Biochemistry 44 (2005) 16988-16997
62. Remeta D.P., Mudd C.P., Berger R.L., and Breslauer K.J. Thermodynamic characterization of daunomycin DNA Interactions- microcalorimetric measurements of daunomycin DNA-binding enthalpies. Biochemistry 30 (1991) 9799-9809